BN9944 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 6.6765e-05 3.5296e-03
Layer 5 1.0617e-04 1.7851e-03
Layer 6 8.0552e-04 7.0220e-03
Layer 3 8.1753e-04 6.0866e-02
Layer 2 1.3372e-02 2.0521e-01
WM 2.2382e-01 3.5162e-01
Layer 1 5.9059e-01 4.9382e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.3867 0.6886
SH3GL2 Layer 5 2.2969 0.6278
SMYD2 Layer 5 2.5332 0.5820
SSBP3 Layer 5 2.5605 0.5812
CLSTN2 Layer 5 2.7852 0.5778
NUDT4 Layer 5 2.3711 0.5489
STX1A Layer 5 2.4297 0.5437
DIRAS2 Layer 6 2.6660 0.5419
PCP4 Layer 5 2.6953 0.5416
TBR1 Layer 6 2.2930 0.5384
KCNAB1 Layer 5 2.1445 0.5378
RAB3C Layer 5 2.4785 0.5363
B4GAT1 Layer 5 2.2363 0.5358
SYN2 Layer 5 2.2969 0.5330
EFHD2 Layer 5 2.3965 0.5328
NAP1L3 Layer 5 2.2715 0.5319
UBE2QL1 Layer 4 2.2969 0.5316
TUBB Layer 5 2.3125 0.5292
ATP6V0D1 Layer 5 2.3496 0.5244
SLC25A22 Layer 5 2.2461 0.5227
SNAP91 Layer 5 2.3594 0.5227
CD24 Layer 5 2.1816 0.5225
ANXA6 Layer 5 2.3086 0.5223
HS3ST2 Layer 5 2.3652 0.5210
TUBB2A Layer 5 2.2227 0.5204
SLC24A2 Layer 5 2.3438 0.5204
CAMK2D Layer 5 2.4609 0.5190
STMN2 Layer 5 2.1875 0.5187
SYP Layer 5 2.3184 0.5155
SYT4 Layer 6 2.4023 0.5141
CXXC5 Layer 4 2.2129 0.5126
DCLK1 Layer 5 2.2676 0.5106
G3BP2 Layer 5 2.2422 0.5100
SPOCK1 Layer 6 2.3398 0.5089
PNMA8B Layer 5 2.4082 0.5088
CAMK2G Layer 5 2.2266 0.5085
SEZ6L2 Layer 4 2.1484 0.5078
FAM3C Layer 5 2.6484 0.5073
SYNGR1 Layer 5 2.2266 0.5060
CTSD Layer 5 2.1914 0.5059
CEND1 Layer 5 2.1387 0.5058
ZBTB16 Layer 4 2.1680 0.5048
MAP1LC3A Layer 5 2.2168 0.5041
IQSEC1 Layer 5 2.2461 0.5037
PCDH10 Layer 5 2.1484 0.4996
CHGB Layer 5 2.0547 0.4994
KLHDC3 Layer 5 2.1387 0.4991
CDK14 Layer 5 2.2617 0.4981
PDE1A Layer 5 2.3555 0.4965
CPLX1 Layer 5 2.1914 0.4965

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN9944
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN9944_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9944/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9944/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9944/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9944/report/PD/BN9944_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9944/report/PD/BN9944_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:59:55
  • Number of Processes: 10
  • Spending Time: 0h 5m